Micro‐Topographies Induce Epigenetic Reprogramming and Quiescence in Human Mesenchymal Stem Cells

Abstract Biomaterials can control cell and nuclear morphology. Since the shape of the nucleus influences chromatin architecture, gene expression and cell identity, surface topography can control cell phenotype. This study provides fundamental insights into how surface topography influences nuclear morphology, histone modifications, and expression of histone‐associated proteins through advanced histone mass spectrometry and microarray analysis. The authors find that nuclear confinement is associated with a loss of histone acetylation and nucleoli abundance, while pathway analysis reveals a substantial reduction in gene expression associated with chromosome organization. In light of previous observations where the authors found a decrease in proliferation and metabolism induced by micro‐topographies, they connect these findings with a quiescent phenotype in mesenchymal stem cells, as further shown by a reduction of ribosomal proteins and the maintenance of multipotency on micro‐topographies after long‐term culture conditions. Also, this influence of micro‐topographies on nuclear morphology and proliferation is reversible, as shown by a return of proliferation when re‐cultured on a flat surface. The findings provide novel insights into how biophysical signaling influences the epigenetic landscape and subsequent cellular phenotype.

FCP Fraction of the feature area covered by primitives.

Patt ern area
The product of the feature size and the FCP.

Num Circ
Number of circles in the feature.

Num Tri
Number of triangles in the feature.

Num Line
Number of lines in the feature.

Circ Dia m
The diameter of the circle(s) in the feature area.

Line Len
The length of the line(s) in the feature area.

TriSi ze
Shortest side length of a triangle primitive.
DC The density of the circle primitives in a feature. Calculated by dividing the total number of circles by the feature size of the feature. DT The density of the triangle primitives in a feature. Calculated by dividing the total number of circles by the feature size of the feature. DL The density of the line primitives in a feature. Calculated by dividing the total number of circles by the feature size of the feature. CA The product of the density of circle primitives (DT) in a feature and the area of the circle primitive.
TA The product of the density of triangle primitives (DC) in a feature and the area of a triangle primitive.
LA The product of the density of line primitives (DL) in a feature and the area of a line primitive.
CCD CCD is defined as the number of times a primitive is encountered starting over the diagonal from the bottom left corner to the top right corner divided by the length of this diagonal in µm.

WN X
A two-dimensional discrete Fourier transformation representing the elements of the discretization of the feature as a sum of sinusoids with different wavenumbers. Eleven variables WNX with values ranging from 0.1 to 4 were created. These variables represent the fraction of the total energy that is present in sinusoids with wavenumber X. .E.g. a high value for WN0.1 represents features containing relatively much energy in sinusoids with a low wavenumber.  Perimeter The total number of pixels around the boundary of each region in the image.
Solidity Solidity: The proportion of the pixels in the convex hull that are also in the object, i.e. ObjectArea/ConvexHullArea. Equals 1 for a solid object (i.e., one with no holes or has a concave boundary), or <1 for an object with holes or possessing a convex/irregular boundary. Extent Extent: The proportion of the pixels in the bounding box that are also in the region. Computed as the Area divided by the area of the bounding box.

EulerNumb er
EulerNumber: The number of objects in the region minus the number of holes in those objects, assuming 8connectivity.

Center_X, Center_Y
Center_X, Center_Y: The x-and y-coordinates of the point farthest away from any object edge. Note that this is not the same as the Location-X and -Y measurements produced by the Identify modules.

Eccentricit y
Eccentricity: The eccentricity of the ellipse that has the same second-moments as the region. The eccentricity is the ratio of the distance between the foci of the ellipse and its major axis length. The value is between 0 and 1. (0 and 1 are degenerate cases; an ellipse whose eccentricity is 0 is actually a circle, while an ellipse whose eccentricity is 1 is a line segment.)

MajorAxis Length
MajorAxisLength: The length (in pixels) of the major axis of the ellipse that has the same normalized second central moments as the region.

MinorAxis Length
MinorAxisLength: The length (in pixels) of the minor axis of the ellipse that has the same normalized second central moments as the region. Orientation Orientation: The angle (in degrees ranging from -90 to 90 degrees) between the x-axis and the major axis of the ellipse that has the same second-moments as the region.

Compactne ss
Compactness: The variance of the radial distance of the object's pixels from the centroid divided by the area.

MaximumR adius
MaximumRadius: The maximum distance of any pixel in the object to the closest pixel outside of the object. For skinny objects, this is 1/2 of the maximum width of the object.

MedianRad ius
MedianRadius: The median distance of any pixel in the object to the closest pixel outside of the object.

MeanRadiu s
MeanRadius: The mean distance of any pixel in the object to the closest pixel outside of the object.

MinFeretDi ameter, MaxFeretD iameter
MinFeretDiameter, MaxFeretDiameter: The Feret diameter is the distance between two parallel lines tangent on either side of the object (imagine taking a caliper and measuring the object at various angles). The minimum and maximum Feret diameters are the smallest and largest possible diameters, rotating the calipers along all possible angles.